Marquez set a record lap time of 1:58.867 at pre-season testing in Sepang, but Hernandez is confident the world champion's bike can be improved upon before the season kicks off.
Hernandez was speaking to Movistar TV.
He said: "Like last year, the best point is the braking, especially on corner entry, but we still need to improve cornering and especially the exit, in order to have more grip.
"With the rear is where we struggle more, especially on fast corners, where the Yamaha is better, as we saw last year at this circuit. But Honda is doing a good job and I think that at the next test we will have something that can help us."
Hernandez added: "The configuration of this engine compared to last year is a little different, especially in terms of the power delivery.
"The engine is more aggressive, so on the corners and especially on the fast corners it means there are some grip problems when taking the corner. But we're not too worried. It is working well and there is still the second test in Sepang and the test in Qatar to come, so that we can get to the first race in the best condition."